ABSTRACT
ObjectiveTo conduct genetic variation analysis of 11 cultivars and 7 wild populations of Angelica sinensis in Gansu province based on the chloroplast gene （cp DNA）， and provide references for germplasm identification and breeding of new cultivars of A. sinensis. MethodThree pairs of cp DNA primers were used for polymerase chain reaction （PCR） amplification and sequencing of A. sinensis samples. MegaX was used to perform statistics on sequence characteristics and calculate mean genetic distances among A. sinensis populations. Unweighted pair-group method with arithmetic means （UPGMA） clustering tree based on genetic distance was constructed by NTSYS 2.10e. DanSP v6 was used to calculate sequence polymorphism and Tajima's D of A. sinensis. PERMUT was used to calculate the population structure of A. sinensis. Arlequin v3.5 was used to perform molecular variation analysis， and PopART1.7 was used to construct TCS haplotype network. ResultThree pairs of cp DNA primers were amplified， sequenced， compared， and combined to give a sequence length of 1 759 bp. One variable site was detected in the wild A. sinensis and 480 variable sites were detected in the cultivated A. sinensis， including 97 singleton variable sites， 383 parsimony informative sites， and 152 insertion-deletion sites. In the three regions of matK， psbA-trnH， and rbcL of cp DNA in the wild and cultivated A. sinensis， matK was the region with the highest polymorphism. Tajima’s D of all the combined sequences of A. sinensis were not significantly negative， but psbA-trnH and rbcL genes of the cultivated A. sinensis were significantly negative， indicating that the A. sinensis followed neutral evolution on a whole， while psbA-trnH and rbcL genes had undergone selection. The degree of genetic differentiation （Fst=0） among wild populations was lower than that among cultivated populations （Fst=0.114 19， P<0.05）. The degree of genetic differentiation between wild and cultivated A. sinensis was relatively high （Fst=0.942 55， P<0.01）. Genetic variation in the cultivated A. sinensis was mainly found within the populations （89%）. UPGMA cluster tree based on genetic distance showed that the wild A. sinensis and the cultivated A. sinensis were clustered into one branch， respectively， with a distant genetic relationship， and the population 3 in the cultivated A. sinensis was far from other cultivated populations. The TCS haplotype network consisted of 15 haplotypes and 4 unknown haplotypes， which was divided into 3 parts， with a large number of variations among each part. Shared haplotypes were only found in the wild or cultivated groups， and there were no shared haplotypes between groups. ConclusionThe genetic diversity of A. sinensis was low at species level， and the population diversity of the wild was lower than that of the cultivated. The degree of genetic differentiation between the wild and the cultivated A. sinensis was high， but that in the wild and the cultivated populations were low. Genetic variation in the cultivated A. sinensis was mainly found within populations.
ABSTRACT
ObjectiveTo analyze the sequence variation and genetic diversity of 47 Isatis indigotica germplasm materials， and carry out the study on the genetic differentiation and structure. MethodGenomic DNA of 47 I. indigotica germplasm materials were extracted by kit extraction method. Two chloroplast DNA （cp DNA） sequences and five inter-simple sequence repeat （ISSR） primers were used for amplification and sequencing. Chromas， Mega 7.0， DanSP5， and GenALEx were used to calibrate， splice， and analyze the sequence characteristics. PERMUT and PopGen 1.31 were used to analyze the genetic diversity parameters and genetic structure， and NTSYS was used to obtain the unweighted pair-group method with arithmetic means（UPGMA） clustering tree plot of 47 I. indigotica germplasm materials. ResultA total of 129 samples from 47 I. indigotica germplasm materials were successfully amplified and sequenced. The length of 2 cp DNA sequences after spliced was 1 412 bp， and there were 377 polymorphic variation loci， and 36 haplotypes. Fu and Li's D* test was significant （P<0.01）. The values of Pi， HS， and HT based on cp DNA were 0.119 89， 0.787， and 0.891， respectively. The genetic differentiation coefficients of gene differentiation coefficient（Gst）， nucleotide differentiation coefficient（Nst）， and fixation index（Fst） were 0.117， 0.468， and 0.488， respectively， and the gene flow （Nm） was 0.615. The mean values of PPB， Shannon information diversity index（I）， Nei's genetic diversity index（H）， and Gst based on ISSR were 78.85%， 0.334 8， 0.218 6， and 0.754 4， respectively， and the Nm value was 0.162 8. ConclusionI. indigotica has high genetic diversity and abundant haplotypes at the species level， with abundant haplotypes. Genetic differentiation among different germplasm materials is obvious， and gene exchange is not frequent. Genetic variation mainly exists among populations. The population has accumulated various low-frequency gene mutations recently， suggesting that it has experienced significant regional expansion in the history.
ABSTRACT
ObjectiveTo analyze the sequence variation and genetic diversity of 47 Isatis indigotica germplasm materials， and carry out the study on the genetic differentiation and structure. MethodGenomic DNA of 47 I. indigotica germplasm materials were extracted by kit extraction method. Two chloroplast DNA （cp DNA） sequences and five inter-simple sequence repeat （ISSR） primers were used for amplification and sequencing. Chromas， Mega 7.0， DanSP5， and GenALEx were used to calibrate， splice， and analyze the sequence characteristics. PERMUT and PopGen 1.31 were used to analyze the genetic diversity parameters and genetic structure， and NTSYS was used to obtain the unweighted pair-group method with arithmetic means（UPGMA） clustering tree plot of 47 I. indigotica germplasm materials. ResultA total of 129 samples from 47 I. indigotica germplasm materials were successfully amplified and sequenced. The length of 2 cp DNA sequences after spliced was 1 412 bp， and there were 377 polymorphic variation loci， and 36 haplotypes. Fu and Li's D* test was significant （P<0.01）. The values of Pi， HS， and HT based on cp DNA were 0.119 89， 0.787， and 0.891， respectively. The genetic differentiation coefficients of gene differentiation coefficient（Gst）， nucleotide differentiation coefficient（Nst）， and fixation index（Fst） were 0.117， 0.468， and 0.488， respectively， and the gene flow （Nm） was 0.615. The mean values of PPB， Shannon information diversity index（I）， Nei's genetic diversity index（H）， and Gst based on ISSR were 78.85%， 0.334 8， 0.218 6， and 0.754 4， respectively， and the Nm value was 0.162 8. ConclusionI. indigotica has high genetic diversity and abundant haplotypes at the species level， with abundant haplotypes. Genetic differentiation among different germplasm materials is obvious， and gene exchange is not frequent. Genetic variation mainly exists among populations. The population has accumulated various low-frequency gene mutations recently， suggesting that it has experienced significant regional expansion in the history.